Yeah there will be plenty off issues using npm. The native npm packages will most likely break. Npm has support for binary builds but I'm not sure most packages will have a completely separate build process set up for windows.

In the case of the mongodb package I'm deprecating the c++ bson parser as the js parser is as fast or faster than the c++ bson parser (v8 crankshaft and fast arrays rock) and this "should" make it work out of the box on the windows node.js build (crossing fingers)